Is it permissible for one to shake hands with his uncle`s daughter?

No, it isn`t because he is a non-Mahram (Marriageable) to her.

Is it permissible for a woman whose menses exceeded (15) days to pray, fast and do what was prohibited on her to do during the latter period?

If the menses exceeded 15 days then it is deemed menstruation, and in this case she is obliged to pray and fast and to do what was impermissible for her to do during the latter period. In addition, she is obliged to make an ablution for each obligatory prayer after it's due time and making sure that impuity is removed. Finally, your menstruation period is over (Questioner) simlar to your menstruation in the previos month.

During Ramadan, a man had sexual intercourse with his wife. What is the expiation for that? And is he permitted to pay the expiation?

Is it permissible for me to eat from the animal that I slaughtered for Allah to protect my family?

It is permissible to eat from the non-vowed animal sacrifice, and the person is rewarded based on the amount of meat that he had given to the poor. However, there is no evidence in Islamic Sharia indicating that slaughtering an animal protects one`s family, but it is a way for thanking Allah, The Almighty, for his grace.